1. The make of QTLdb calls for a trait ontology
Part II
The make of QTLdb calls for
a trait ontology
(Development of a trait ontology prototype)
Zhiliang Hu and James Reecy
Iowa State University

2. Trait measurement variations, e.g. Backfat
Animal Trait Ontology
Trait measurement variations, e.g. Backfat
Backfat Thickness (Average Backfat) by ruler
Backfat Thickness (Average Backfat) by ultrasound
Backfat Thickness (Average Backfat) by Fat-O-Meater
Backfat at First Rib (First Rib Backfat)
Backfat at First Rib (Measured at 14 Weeks of Age)
Backfat at First Rib (Measured at 26 Weeks of Age)
Backfat at Last Rib (Measured at 14 Weeks of Age)
Backfat at Last Rib (Measured at 26 Weeks of Age)
Backfat Thickness at Last Rib
Backfat at Shoulder
Backfat at Tenth Rib
Backfat between 3th and 4th Rib
Backfat between 6th and 7th Rib
Backfat Depth at Max. Mus. Depth
Backfat at Last Lumbar
Backfat weight (dissected total weight)
……….
by methods
by time
by locations

3. Animal Trait Ontology Trait definitions ? Trait types ?
Trait categories ?

4. Animal Trait Ontology
Trait names are defined with actual terms that closely represent the concept of a trait.
Trait description and measurement criteria are information expanded from trait names to describe the detailed criteria in which a trait is recorded.
Trait type (“super trait”) describes physical or a chemical property of the pork products, or feature that can influence the process in which a pork product is made, for example, backfat, ADG, muscle pH, feed intake, etc.
Trait category describes very general aspects of pork products, or processes in which the product is made, for example, meat quality, health, growth, reproduction, etc.

5. Revisit the Pig traits in the QTLdb
Animal Trait Ontology
Revisit the Pig traits in the QTLdb
Controlled vocabulary
Trait classification hierarchy
5 categories
25 trait types (super-traits)
236 traits
Zhiliang Hu, Svetlana Dracheva, Wonhee Jang, Donna Maglott, John Bastiaansen, Max F. Rothschild and James M. Reecy (2005). A QTL resource and comparison tool for pigs: PigQTLDB. Mammalian Genome. Volume 16(10):

6. Animal Trait Ontology New challenges:
What’s the best way to classify the trait data?
What’s the best way to organize the trait data?
What’s the best way to manage the trait data?
For example, is “backfat”
A growth trait ?
A meat quality trait ?
A health trait ?
Or does it matter anyway ?

7. Animal Trait Ontology Ontology: Data Management
A description of concepts and relationships
For the purpose of enabling knowledge sharing and re-use
Ontological commitment is an agreement to use a vocabulary
Data Management
Ways to house the data (Word processor; Spread sheet; Database; etc.)
Ways to modify the data (Definitions, Descriptions, Relationships, etc.) in a coorperative way

8. Animal Trait Ontology Editor
Project web site and software download:
Collaborative Ontology Building (COB) editor
For more details and discussions
For further development of ATO
From “Traits” to “Phenotypes”
A community effort is needed

9. Acknowledgement Max Rothschild (Iowa State University)
John Bastiaansen (former PIC)
Jie Bao (Dept of Computer Sci., Iowa State University)
LaRon Hughes (Dept of Animal Sci., Iowa State University)